Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome_awesome_chemoinformatics
https://github.com/mkorshe/awesome_awesome_chemoinformatics
- https://github.com/Bin-Chen-Lab/Awesome_BigData_AI_DrugDiscovery
- https://github.com/LeeJunHyun/The-Databases-for-Drug-Discovery
- https://github.com/lmmentel/awesome-python-chemistry
- https://github.com/hsiaoyi0504/awesome-cheminformatics
- http://polysearch.cs.ualberta.ca/otherdatabases
- https://www.click2drug.org/ - the biggest list of tools and resources for drug discovery
- Learncheminformatics.com - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.
- Python for chemoinformatics
- TeachOpenCADD - A teaching platform for computer-aided drug design (CADD) using open source packages and data.
- Cheminformatics OLCC - Cheminformatics course of the Collaborative Intercollegiate Online Chemistry Course (OLCC) course of University of Arkansas at Little Rock by Robert Belford
- BigChem - All lectures of [BigChem](http://bigchem.eu/) (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)
- Molecular modeling course - by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis.
- Simulation in Chemistry and Biochemistry - by Dr. [Jay Ponder](https://dasher.wustl.edu/), a professor from WashU St.Louis.
- Computational Approaches in Cheminformatics and Bioinformatics - Include insights from public (NIH), academic, and industrial sources at the same time.
- Chemoinformatics for Drug Discovery - Materials about how to use Chemoinformatics strategies to improve drug discovery results.
- Molecular Descriptors for Chemoinformatics - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.
- Open Source Molecular Modeling - Updateable catalog of open source molecular modeling software.
- PubChem Blog - News, updates and tutorials about [PubChem](https://pubchem.ncbi.nlm.nih.gov/).
- The ChEMBL-og blog - Stories and news from Computational Chemical Biology Group at [EMBL-EBI](https://www.ebi.ac.uk/).
- ChEMBL blog - ChEMBL on GitHub.
- SteinBlog - Blog of [Christoph Steinbeck](http://www.steinbeck-molecular.de/steinblog/index.php/about/), who is the head of cheminformatics and metabolism at the EMBL-EBI.
- Practical Cheminformatics - Blog with in-depth examples of practical application of cheminformatics.
- Noel O'Blog - Blog of [Noel O'Boyle](https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software.
- chem-bla-ics - Blog of [Egon Willighagen](http://egonw.github.io/), who is an assistant professor at Maastricht University.
- steeveslab-blog - Some examples using [RDKit](http://www.rdkit.org/).
- Macs in Chemistry - Provide a resource for chemists using Apple Macintosh computers.
- DrugDiscovery.NET - Blog of [Andreas Bender](http://www.andreasbender.de/), who is a Reader for Molecular Informatics at University of Cambridge.
- Is life worth living? - Some examples for cheminformatics libraries.
- Cheminformatics 2.0 - Blog of [Alex M. Clark](https://twitter.com/aclarkxyz), a research scientist at Collaborative Drug Discovery.
- Depth-First - Blog of [Richard L. Apodaca](https://depth-first.com/about/), a chemist living in La Jolla, California.
- batchcalculator - A GUI app based on wxPython for calculating the correct amount of reactants (batch) for a particular composition given by the molar ratio of its components.
- cctbx - The Computational Crystallography Toolbox.
- chemlib - A robust and easy-to-use package that solves a variety of chemistry problems.
- chempy - ChemPy is a package useful for chemistry (mainly physical/inorganic/analytical chemistry).
- GoodVibes - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.
- ionize - Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions.
- mendeleev - A package that provides a python API for accessing various properties of elements from the periodic table of elements.
- Open Babel - A chemical toolbox designed to speak the many languages of chemical data.
- periodictable - This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.
- propka - Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
- pybel - Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python.
- pycroscopy - Scientific analysis of nanoscale materials imaging data.
- pyEQL - A set of tools for conventional calculations involving solutions (mixtures) and electrolytes.
- pyiron - pyiron - an integrated development environment (IDE) for computational materials science.
- pymatgen - Python Materials Genomics is a robust, open-source library for materials analysis.
- symfit - a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data.
- symmetry - Symmetry is a library for materials symmetry analysis.
- stk - A library for building, manipulating, analyzing and automatic design of molecules.
- amp - Is an open-source package designed to easily bring machine-learning to atomistic calculations.
- Atomic Silumation Environment (ASE) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
- basis_set_exchange - A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data.
- CACTVS - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.
- ccdc - An API for the Cambridge Structural Database System.
- cclib - A library for parsing output files various quantum chemical programs.
- cinfony - A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices).
- chainer-chemistry - A Library for Deep Learning in Biology and Chemistry.
- chemlab - Is a library that can help the user with chemistry-relevant calculations.
- chemml - A machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data.
- deepchem - Deep-learning models for Drug Discovery and Quantum Chemistry.
- emmet - A package to 'build' collections of materials properties from the output of computational materials calculations.
- fromage - The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment.
- GPAW - Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
- horton - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians.
- Indigo - Universal cheminformatics libraries, utilities and database search tools.
- MAML - Aims to provide useful high-level interfaces that make ML for materials science as easy as possible.
- mathchem - Is a free open source package for calculating topological indices and other invariants of molecular graphs.
- MDAnalysis - Is an object-oriented library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
- MDTraj - Package for manipulating molecular dynamics trajectories with support for multiple formats.
- MMTK - The Molecular Modeling Toolkit is an Open Source program library for molecular simulation applications.
- MolMod - A library with many components that are useful to write molecular modeling programs.
- OPEM - Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.
- pGrAdd - A library for estimating thermochemical properties of molecules and adsorbates using group additivity.
- phonopy - An open source package for phonon calculations at harmonic and quasi-harmonic levels.
- PLAMS - Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.
- pMuTT - A library for ab-initio thermodynamic and kinetic parameter estimation.
- PorePy - A Simulation Tool for Fractured and Deformable Porous Media.
- ProDy - An open source package for protein structural dynamics analysis with a flexible and responsive API.
- Psi4 - A hybrid Python/C++ open-source package for quantum chemistry.
- pyEMMA - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data.
- pygauss - An interactive tool for supporting the life cycle of a computational molecular chemistry investigations.
- PyQuante - Is an open-source suite of programs for developing quantum chemistry methods
- pysic - A calculator incorporating various empirical pair and many-body potentials.
- Pyscf - A quantum chemistry package written in Python.
- pyvib2 - A program for analyzing vibrational motion and vibrational spectra.
- RDKit - Open-Source Cheminformatics Software.
- ReNView - Usage-Instructions) - A program to visualize reaction networks.
- stk - A library for building, manipulating, analyzing and automatic design of molecules.
- QUIP - A collection of software tools to carry out molecular dynamics simulations.
- tsase - The library which depends on ASE to tackle transition state calculations.
- ase-gui - The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects.
- chemview - An interactive molecular viewer designed for the IPython notebook.
- imolecule - An embeddable webGL molecule viewer and file format converter.
- nglview - A [Jupyter](https://jupyter.org/) widget to interactively view molecular structures and trajectories.
- PyMOL - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
- pymoldyn - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices.
- sumo - A toolkit for plotting and analysis of ab initio solid-state calculation data.
- surfinpy - A library for the analysis, plotting and visualisation of ab initio surface calculation data.
- ChemSpiPy - [ChemSpider](http://www.chemspider.com/) wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
- CIRpy - An interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH.
- pubchempy - PubChemPy provides a way to interact with PubChem in Python.
- http://zinc.docking.org/
- https://clue.io/cmap
- https://pubchem.ncbi.nlm.nih.gov/
- https://www.rcsb.org/
- https://www.ncbi.nlm.nih.gov/geo/
- https://www.pharmgkb.org/
- http://stitch.embl.de/
- https://www.rdkit.org/
- http://snap.stanford.edu/decagon/
- https://deepchem.io/
- https://github.com/deepchem/deepchem
- https://arxiv.org/abs/1703.00564
- https://www.drugbank.com/
- https://www.drugbank.ca/
- https://string-db.org/
- https://github.com/IBM/InterpretableDTIP
- https://www.bindingdb.org/bind/index.jsp
- http://sideeffects.embl.de/
- https://www.ebi.ac.uk/chembl/
- https://www.ebi.ac.uk/chembl/beta/
- https://chembl.gitbook.io/chembl-interface-documentation/downloads
- http://db.idrblab.net/ttd/
- http://www.pdbbind.org.cn/
- https://tripod.nih.gov/tox21/challenge/data.jsp
- http://gdb.unibe.ch/downloads/
- http://quantum-machine.org/datasets/
- https://peptone.io/dspp
- http://www.cuilab.cn/hmdd
- https://drugtargetcommons.fimm.fi/
- https://druggablegenome.net/
- https://pharos.nih.gov/idg/index
- BioNLP Challenge
- BioNLP Kaggle
- http://polysearch.cs.ualberta.ca/
- BioNLP
- http://cpdb.molgen.mpg.de/
- http://chemdataextractor.org/
Programming Languages
Keywords
chemistry
5
cheminformatics
4
python
4
materials-science
3
deep-learning
3
computational-chemistry
2
machine-learning
2
quantum-chemistry
2
simulation
2
drug-discovery
2
bingo
1
dotnet
1
inchi
1
indigo
1
java
1
microsoft-sql-server
1
molfile
1
oracle
1
postgresql
1
smarts
1
smiles
1
webassembly
1
quantum-mechanics
1
materials-informatics
1
data-science
1
scikit-learn
1
rdkit
1
jupyter
1
chemoinformatics
1
bioinformatics
1
awesome-list
1
awesome
1
python-chemistry
1
molecular-dynamics
1
thermdat
1
thermochemistry
1
discretization
1
finite-volume-methods
1
fractures
1
porous-media
1
virtual-elements
1
biology
1
computational-science
1
materials-design
1
materials-discoveries
1
materials-screening
1
molecular-evolution
1
molecular-modeling
1
molecular-structures
1
reactions
1